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The song is known for its distinct time signatures and corresponding lyrical patterns. The time signatures of the chorus of the song change from 9/8 to 8/8 to 7/8; as drummer Danny Carey says, "It was originally titled 9-8-7. For the time signatures. Then it turned out that 987 was the 16th number of the Fibonacci sequence. So that was cool."[2]

In a 2001 interview, singer Maynard James Keenan commented on the lyric mentioning black, white, red and yellow: "I use the archetype stories of North American aboriginals and the themes or colours which appear over and over again in the oral stories handed down through generations. Black, white, red, and yellow play very heavily in aboriginal stories of creation."[3]

The song could also be about the order of colors seen while under the influence of LSD. Alex Grey (the visionary artist who did the album artwork for Lateralus) stated that when he closed his eyes on an LSD trip, he saw a black and white spiral, and when he tried it a few more times it became a red and yellow spiral.[4]

The line "As below so above and beyond, I imagine" is a quote from one of the Seven Aphorisms of Summum and is also a direct reference to Hermeticism and the Emerald Tablet.

An interesting side note, in alchemy "The Great Work" begins with the Nigredo (black), then moves to the Albedo (white), then the Citrinitas (yellow), then the Rubedo (Red).

Counting between pauses, the syllables in Maynard James Keenan's vocals during the verses form the first few Fibonacci numbers, ascending and descending. For instance, in the first verse: "Black, then, white are, all I see, in my infancy. Red and yellow then came to be." correspond with the beginning of the sequence: (1, 1, 2, 3, 5, 8).[3][5]

The song's introduction also ends at the 1 minute and 37 mark, where the first verse then begins. This time is significant as it is a reference to the Golden Ratio. Rounding the Golden Ratio to four places gives 1.618. When converted to minutes and seconds, the Golden Ratio becomes 1 minute + 0.618ths of a minute; which after rounding and conversion is equal to approximately 37 seconds. This also ties it to the Fibonacci sequence as the ratio of one Fibonacci number to its predecessor tends towards the Golden Ratio.